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- EMDB-14885: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN -

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Basic information

Entry
Database: EMDB / ID: EMD-14885
TitleOMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Map data
Sample
  • Complex: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
    • Complex: SARS-COV-2 BETA SPIKE GLYCOPROTEIN
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: OMI-42 FAB
      • Protein or peptide: Omi-42 heavy chain
      • Protein or peptide: Omi-42 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-COV2 / SPIKE / GLYCOPROTEIN / ANTIBODY / FAB / B.1.135 / BETA VARIANT / COMPLEX / NEUTRALISING / CONVALESCENT SERA / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / IMMUNE SYSTEM COMPLEX / STRUCTURAL PROTEIN
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDuyvesteyn HME / Ren J / Stuart DI
Funding support China, United Kingdom, 3 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018-I2M-2-002 China
Medical Research Council (MRC, United Kingdom)MR/N00065X/1) United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CitationJournal: Cell / Year: 2022
Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
History
DepositionMay 3, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14885.png

Downloads & links

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Map

FileDownload / File: emd_14885.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 420 pix.
= 697.2 Å		1.66 Å/pix.
x 420 pix.
= 697.2 Å		1.66 Å/pix.
x 420 pix.
= 697.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3457861 - 0.90762854
Average (Standard dev.)-0.00023395776 (±0.011899964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 697.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14885_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14885_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN

EntireName: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
Components
  • Complex: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
    • Complex: SARS-COV-2 BETA SPIKE GLYCOPROTEIN
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: OMI-42 FAB
      • Protein or peptide: Omi-42 heavy chain
      • Protein or peptide: Omi-42 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN

SupramoleculeName: OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: SARS-COV-2 BETA SPIKE GLYCOPROTEIN

SupramoleculeName: SARS-COV-2 BETA SPIKE GLYCOPROTEIN / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: OMI-42 FAB

SupramoleculeName: OMI-42 FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 141.993984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String:
MFVFLVLLPL VSSQCVNFTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFA NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRGLPQ GFSALEPLVD LPIGINITRF QT LHISYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFG EVFNATRFAS VYAWNRKRIS NCVADYSVLY NSASFSTFKC YGVSPTKLND LCFTNVYADS FVIR GDEVR QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NNLDSKVGGN YNYLYRLFRK SNLKPFERDI STEIYQAGST PCNGV KGFN CYFPLQSYGF QPTYGVGYQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEH VNNSYECDIP IGAGICASYQ TQTNSPGSAS SVASQSIIAY TMSLGVENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLN RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KDFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NQNAQALNTL V KQLSSNFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHG SAWSHPQFEK GGGSGGGSGG SAWSH PQFE K

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #2: Omi-42 heavy chain

MacromoleculeName: Omi-42 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.541031 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLLETGGG LVQPGRSLRL SCAASGFPFD DYAIHWVRLA PGKGLEWVSS ISWDSGSIGY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYYCAKG AFPGYSSGWY YGLDVWGQGA TVTVSS

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Macromolecule #3: Omi-42 light chain

MacromoleculeName: Omi-42 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.286393 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVVTQPPSA SGSLGQSVTI SCTGTSSDVG GYNYVSWYQQ HPGKAPKLMI FEVSKRPSGV PDRFSGSKSG NTASLTVSGL QAEDEADYY CSSYAGNKGV FGGGTKLTVL

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio volume.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Determined in cryoSPARC / Number images used: 106884
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7q9g


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 213.7 / Target criteria: Correlation coefficient
Output model

PDB-7zr7:
OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN

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